Variant report

Variant	rs9458257
Chromosome Location	chr6:161863950-161863951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12196262	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205669	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17647667	0.85[CEU][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs7770642	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771517	0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774827	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458254	0.84[ASW][hapmap];0.92[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9458255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458256	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458258	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv481931	chr6:161647026-161961906	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1031234	chr6:161676768-162250726	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv886819	chr6:161712035-162520133	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv886820	chr6:161712880-162184932	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv830854	chr6:161739926-161927515	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv518931	chr6:161793319-162406335	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv481861	chr6:161802883-162160197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv481981	chr6:161829077-162215745	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1033603	chr6:161844266-162001436	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv481750	chr6:161850976-161996586	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv481932	chr6:161862158-162097499	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9458257	AGPAT4	cis	cerebellum	SCAN
rs9458257	SLC22A2	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161855600-161864400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161856600-161866200	Weak transcription	Psoas Muscle	Psoas
3	chr6:161860400-161864400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:161860400-161864800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:161860400-161866200	Weak transcription	Esophagus	oesophagus
6	chr6:161860600-161864800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:161860600-161864800	Weak transcription	Pancreas	Pancrea
8	chr6:161860600-161864800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:161860600-161865000	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:161860600-161865000	Weak transcription	Ovary	ovary
11	chr6:161860600-161865200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:161860600-161871000	Weak transcription	Right Atrium	heart
13	chr6:161860800-161864400	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:161860800-161864800	Weak transcription	Brain Anterior Caudate	brain
15	chr6:161860800-161864800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:161860800-161864800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:161860800-161864800	Weak transcription	HMEC	breast
18	chr6:161860800-161864800	Weak transcription	HSMMtube	muscle
19	chr6:161860800-161864800	Weak transcription	NH-A	brain
20	chr6:161860800-161865000	Weak transcription	Brain Angular Gyrus	brain
21	chr6:161860800-161865000	Weak transcription	NHDF-Ad	bronchial
22	chr6:161860800-161865200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:161860800-161865200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr6:161860800-161865400	Weak transcription	Osteobl	bone
25	chr6:161861000-161864800	Enhancers	Brain Germinal Matrix	brain
26	chr6:161861000-161865000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:161861000-161865200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr6:161861000-161865400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:161861000-161865400	Weak transcription	Brain Substantia Nigra	brain
30	chr6:161861600-161864800	Weak transcription	Fetal Kidney	kidney
31	chr6:161861800-161864400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:161861800-161864400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:161862000-161864800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:161862200-161865000	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:161862400-161864400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:161862600-161865000	Weak transcription	Spleen	Spleen
37	chr6:161862600-161868600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr6:161862800-161865200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:161862800-161867600	Enhancers	Fetal Brain Male	brain
40	chr6:161863000-161864000	Enhancers	Adipose Nuclei	Adipose
41	chr6:161863000-161866200	Weak transcription	Gastric	stomach
42	chr6:161863400-161864200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:161863400-161864200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:161863400-161865400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:161863400-161867600	Enhancers	HSMM	muscle
46	chr6:161863800-161864800	Weak transcription	Fetal Brain Female	brain
47	chr6:161863800-161864800	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links